I got some hub genes based on PPI network and then I did promoter analysis based on transcription factor binding sites. Let's see I have a list of 50 hub genes and 200 transcription factors. I am gonna visualize this regulatory network using Cytoscape. However, I don't have any idea including 1) how to make input file for network importing on Cytoscape, and 2) how to construct this network on Cytoscape. What am I supposed to do?
Not sure I understand your question completely but I generally "make" the network before loading it into cytoscape. In order to do so I create a table containing a minimum of two columns where column 1 represents node a and column 2 represent node B. This table will encode the network structure. Each row will therefore mark an edge/interaction.
Would represent the following network
You can add additional columns with more information about the interaction e.g. correlation coefficient but this is the most simple way. In cytoscape you can import these networks as csv or tab-delimited tables. Once in cytoscape you will have many options to edit this network, e.g. colors...